Functional deficiency of mannan-binding lectin MBL has been associated with adverse pregnancy outcome. Adverse events during pregnancy have also been described in women with autoimmune thyroid diseases AITD, and thyroid hormones have been shown to influence serum levels of MBL. Therefore, the aim of this study was to analyse the impact of MBL-deficiency on the outcome of pregnancy in relation to the presence of AITD. Almost one year after delivery, we assessed serum MBL levels and MBL2-genotypes in 212 women positively screened for AITD in pregnancy. In 103 of these women, we could also measure MBL levels in frozen serum samples from the 9-12th gestational week, obtaining 96 pairs of MBL values pregnancy vs. follow-up. As controls, 80 sera of pregnant women screened negatively for AITD were used. MBL2-genotyping was performed using multiplex PCR. Women with thyroid dysfunction and-or thyroid peroxidase antibodies TPOAb had lower MBL levels during pregnancy than controls, 3275 vs. 5000 ng-ml, p<0.05. The lowest levels were found in women with elevated thyroid-stimulating hormone TSH levels in the absence of TPOAb 2207 ng-ml; p<0.01 as compared to controls. MBL2 genotype distribution did not differ between subgroups. At a median follow-up period of 17 months range: 3–78 months after delivery, median MBL level had decreased further to 1923 ng-ml p<0.0001 without significant changes in TSH. In an explorative survey, functional MBL-deficiency was neither linked to a history of spontaneous abortion, nor other obstetric complications, severe infections throughout life-pregnancy or antibiotics use in pregnancy. In conclusion, hypothyroidism during pregnancy is associated with decreased MBL levels, and the levels decreased further after delivery.